Download Chapter 5 Proteins - Liberty Public Schools

Proteins
Chapter 3
A. P. Biology
Mr. Knowles
Liberty Senior High School
Proteins are Most Common
Functions of Proteins
1. Enzymes- Metabolism
2. Structural- Collagen and Keratin
3. Cell Recognition- proteins on
cellular surface.
4. Regulation of Gene ExpressionGene Repressors or Enhancers.
5. Defense- Antibodies.
• An overview of protein functions
Table 5.1
Two Types of Proteins
1. Fibrous Proteins- rope-like, structural
proteins; form shape of cells and
tissues. Ex. Collagen-the most
abundant protein of vertebrates.
2. Globular Proteins- have specific
shapes for their functions. Ex.
Enzymes and antibodies.
1. Proteins can be Structural
2. Proteins can be Globular
X-ray crystallography:
Is used to determine a protein’s threedimensional structure.
X-ray
diffraction pattern
Photographic film
Diffracted X-rays
X-ray
X-ray
beam
source
Crystal
Nucleic acid
Figure 5.24
(a) X-ray diffraction pattern
(b) 3D computer model
Protein
Papain
Proteins
• Most diverse organic compound.
• Composed of amino acids- each
with an amino group (NH2) and a
carboxylic acid group (COOH).
• Different chemical group(s)
attached to central C- R group .
Amino
Acid
Polymers
• Amino acids
– Are linked by peptide bonds
Peptide
OH
bond
OH
SH
CH2
CH2
H
N
H
CH2
H
C
C
H
O
N
H
C
C
H
O
OH
H
(a)
N
C
C
H
O
OH
DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
CH2
CH2
H
H
H
Figure 5.18
(b)
N
C
C
H
O
Amino end
(N-terminus)
N
Side chains
SH
Peptide
bond
CH2
OH
H
C
C
H
O
N
C
C
H
O
Carboxyl end
(C-terminus)
OH
Backbone
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
C
H3N+
C
CH
CH3
CH3
O
C
CH3
CH3
CH2
CH2
O
H3N+
C
C
O
H3C
H3N+
C
• 20 different amino acids make up proteins
O–
O–
O–
CH
O
C
C
O–
O–
H
H
H
H
H
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
CH2
O
H3N+
C
C
Methionine (Met)
Figure 5.17
H3
C
O–
O–
H
C
N+
H
Phenylalanine (Phe)
CH2
H2N
C
O
C
O–
CH2
O
H2C
O
H
C
O–
H
Tryptophan (Trp)
Proline (Pro)
OH
NH2 O
C
NH2 O
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
C
CH2
O
H3N+
C
C
CH2
O
C
H3N+
C
Threonine (Thr)
H3N+
C
H
Cysteine
(Cys)
Tyrosine
(Tyr)
O–
O
CH2
H3N+
C
O
H
C
C
C
O
C
O–
O–
H
H
Asparagine
(Asn)
H3N+
NH3+
O
Glutamine
(Gln)
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
CH2
C
O
C
O–
H
H3N+
C
O
C
NH2+
H3N+
C
NH
CH2
H3N+
C
O
C
O–
H
CH2
O–
H
NH+
NH2
C
CH2
C
O–
H3N+
Basic
C
Electrically
charged
CH2
O
O–
H
Acidic
–O
CH2
CH2
O
O–
O–
H
Serine (Ser)
C
SH
CH3
OH
O
C
O–
H
Aspartic acid
(Asp)
Glutamic acid
(Glu)
Lysine (Lys)
Arginine (Arg)
Histidine (His)
Amino Acids
• Are the monomers of proteins.
• Only 20 naturally occurring amino
acids.
• The R group gives each of the
amino acids its unique property.
• All 20 amino acids can be grouped
into 5 basic groups.
5 Groups of Amino Acids
(Fig. 3.15)
1. Nonpolar- have R groups that contain
CH2 and CH3.
2. Polar Uncharged- R groups that have
O or only H.
3. Ionizable- have R groups that are acids
and bases.
4. Aromatic- R groups that have organic
rings.
5 Groups of Amino Acids
(Fig. 3.15)
5. Special-function- amino acids
that are only used for very specific
functions; methionine begins
protein synthesis, proline causes
kinks in the protein polymer,
cysteine links chains together.
The 20 Common Amino
Acids (Fig. 3.15) Click
below for another view!
Proteins
• Are polymers of amino acids.
• Joined by peptide bonds.
• Di- Tri- and Polypeptides.
Globular Proteins
• Are long amino acids chains
folded into complex shapes.
• All of the internal amino acids
are nonpolar.
• Water excludes nonpolar amino
acids – hydrophobic
interactions.
Globular Proteins Have
Four Levels of Structure
1. Primary- the specific sequence of
amino acids in the polypeptide chain.
• R groups have no role in the backbone,
so any sequence of amino acids is
possible.
• Therefore, 100 amino acids may be
rearranged in 20100 different possible
sequences.
Primary Structure:
Is the unique sequence of amino acids
in a polypeptide.
Pro
Gly
Thr
Gly
Thr
+H N
3
Gly
Amino acid subunits
Glu
Amino end
Pro
Leu
Seu
Lys
Cys
Met
Val
Lys
Val
Leu
Asp
Ala
Arg
Val
Gly
Ser
Pro
Ala
Glu
Lle
Asp
Thr
Lys
Ser
Trp
Lys
Ala
Leu
Gly
Tyr
lle
Ser
Pro
Phe
His
Glu
His
Ala
Glu
Ala
Asn
Thr
Phe
Asp
Val
Arg
Ser
Gly
Pro
Val
Tyr
lle
Thr
Ala
Ala
Arg
Leu
Leu
Thr
Ser
Tyr
Ser
Tyr
Pro
Ser
Thr
Ala
o
Val
Val
Figure 5.20
Thr
Asn
Pro
Lys
Glu
c
Carboxyl end
o–
Globular Protein Structure
2. Secondary- folding or coiling of
the chain into a pattern due to weak
H bonds between amino acids.
• H bonds form between the main
chain of amino acids.
• Two Kinds of Secondary Structure
Secondary Structures
• Alpha Helix- H bonds between
one amino acid and another
further down the chain. Pulls the
chain into a coil.
• Beta Sheet- H bonds occur
across two separate chains. If
chains are parallel, they may
form a sheet-like structure.
Secondary Structure:
– Is the folding or coiling of the polypeptide into
a repeating configuration.
– Includes the  helix and the  pleated sheet.
 pleated sheet
H
O
O H
H
R
C C N
Amino acid
subunits
N
C
C C N
C C N
R
O
H
H
C
H
C
H
O
H
N
O C
H
N
O
C
N
C
N
H
O C
H C R H C
H
O C
H C R H C R
R
N
O C
N H
O
H
N
C
C
R
Figure
5.20
O C
C
H
R
H
O C
H
H
C
N
R
H
C
H H
C
 helix
H
C C N
H
O
C C
R
O H H
O
R
C N HC
N
R
R
R
H
R
C C N
O H H
H
O
HC N
O H
H
C C N
R
C
N
R
C C N
R
R
O
O H
H
O
H
C
C
R
R
C
N
H
H
H C N
O
O
H
C
C
R
C
N
H
H
H C N
O
C
Alpha Helix- The First
Type of Secondary
Protein Structure
Beta Sheet- Another
Type of Protein
Secondary Structure
Show me the levels of
protein structure.
Secondary Structures
• Some patterns of alpha helices
and/or beta sheets are very
common in protein structures.
• When secondary structures are
organized into specific structures
within proteins-motifs. Ex. ΒBarrel or α-turn-α motifs
Β-barrel Motif in a Cell
Membrane Protein
Globular Protein Structure
3. Tertiary Structure- folding and
positioning of nonpolar R groups into
the interior of the protein (hydrophobic
interactions).
• Held together by weak van der Waal’s
forces.
• Precise fitting of R groups within the
interior. A change may destabilize a
protein’s shape.
Tertiary Structure:
– Is the overall three-dimensional shape of a
polypeptide.
– Results from interactions between amino acids
and R groups.
Hydrophobic
CH2
CH
2
Hydrogen
bond
O
H
O
interactions and
van der Waals
interactions
CH
H3C
CH3
H3C
CH3
CH
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
Polypeptide
backbone
Globular Protein Structure
4. Quaternary Structure- two or
more polypepetide chains associate
to form a protein.
• Each chain is called a subunit.
• Subunits are not necessarily the
same.
• Ex. Hemoglobin = 2 α-chain
subunits + 2 β-chain subunits.
Quaternary Structure:
– Is the overall protein structure that results from
the aggregation of two or more polypeptide
subunits.
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
The four levels of protein structure
+H N
3
Amino end
Amino
acid
subunits
helix
Quaternary Structure of
Hemoglobin
Hemoglobin structure and sickle-cell
disease
Primary
structure
Normal hemoglobin
Sickle-cell hemoglobin
Primary
Val His Leu Thr Pro Glul Glu . . .
Val His Leu Thr Pro Val Glu . . .
structure 1 2 3 4 5 6 7
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Secondary
 subunit and tertiary
structures

Quaternary Hemoglobin A
structure
Function
Red blood
cell shape
Figure 5.21

Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Quaternary
structure
 subunit




Function
10 m
10 m
Red blood
cell shape
Exposed
hydrophobic
region
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of abnormal
hemoglobin
deform cell into
sickle shape.
Is Protein Folding Important?
Normal Prion
Scrapie Prion
Reverse Transcriptase of HIV
Cobra Toxin
Shape of the Protein
• Tertiary and Quaternary
structures provide shape.
• These structures are maintained
by H bonds and other weak
forces between R groups of
amino acids.
Protein Folding
Conditions that Affect Protein
Shape
Can disrupt H bonds by:
• High Temperature
• pH Changes (Acidic or Basic)
• Ion Concentration (Salt)
Disrupting the 2°, 3°, 4° structure is
called denaturation.
Denaturation:
Is when a protein unravels and loses its
native conformation.
Denaturation
Normal protein
Figure 5.22
Denatured protein
Renaturation
Enzymes:
– Are a type of protein that acts as a
catalyst, speeding up chemical
reactions.
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
2 Substrate binds to
enzyme.
Substrate
(sucrose)
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
Figure 5.16
3 Substrate is converted
to products.
Enzymes are Proteins
• Organic catalysts - increase the
rate of chemical reactions in cells.
• Hold reactant molecules close
together for reaction to occur- uses
an active site.
• The active site is used to bind the
reactant molecules-substrate.
Lock-and-Key Model
Show me the model, Luke!
Write your predictions!
Gelatin =
Substrate
Pineapple =
Papain (Enzyme)